The 49-year-old ex-Norwich City man has served as No.2 to the Manchester United legend on numerous occasions and feels the recently-sacked Leeds boss' barbs were unfair
Following his sacking at Leeds, Warnock said he hoped Hughes would take over from him and "destroy another one of my teams", in reference to Hughes taking over from him at Loftus Road last season.
Bowen jumped to the defence of Hughes, highlighting the standard of playing staff signed by Warnock and the 64-year-old's relatively poor record in the Premier League.
Bowen told reporters: "I'm not going to sugar-coat what went on at the start of the season with Mark's situation. We were 10 games into the season and without a win.
"There are reasons for what has gone on at QPR and what we inherited. We finished the season getting rid of 21 senior players who weren't, with all due respect to them, up to the Premier League.
"Out of all of the players that left not one of them went on to gain a Premier League contract. These are players who Neil Warnock had brought in to the club.
"Everybody knows the club has been in a huge transitional period but it does stick in my throat a bit that Neil has lost another job and started throwing mud around.
"When you look at Mark Hughes's Premier League record, before he went to QPR, it was fabulous, he had never been out of the top 10.
"When you look at Neil Warnock's record, I think the three times he's been in the top leagues he's been relegated twice, with Notts County and Sheffield United, and won the sum total of about 14 Premier League games.
"That's what hurts me the most. There's no need for it, Neil doesn't need to come out and say things like that."